Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data

Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning represents the most cost-effective method for novel AMP discovery and consequently many computational tools for AMP prediction have been recently developed. In this article, we investigate the impact of negative data sampling on model performance and benchmarking. We generated 660 predictive models using 12 machine learning architectures, a single positive data set and 11 negative data sampling methods; the architectures and methods were defined on the basis of published AMP prediction software. Our results clearly indicate that similar training and benchmark data set, i.e. produced by the same or a similar negative data sampling method, positively affect model performance. Consequently, all the benchmark analyses that have been performed for AMP prediction models are significantly biased and, moreover, we do not know which model is the most accurate. To provide researchers with reliable information about the performance of AMP predictors, we also created a web server AMPBenchmark for fair model benchmarking. AMP Benchmark is available at http://BioGenies.info/AMPBenchmark

AmyloGraph : a comprehensive database of amyloid-amyloid interactions

Information about the impact of interactions between amyloid proteins on their fibrillization propensity is scattered among many experimental articles and presented in unstructured form. We manually curated information located in almost 200 publications (selected out of 562 initially considered), obtaining details of 883 experimentally studied interactions between 46 amyloid proteins or peptides. We also proposed a novel standardized terminology for the description of amyloid-amyloid interactions, which is included in our database, covering all currently known types of such a cross-talk, including inhibition of fibrillization, cross-seeding and other phenomena. The new approach allows for more specific studies on amyloids and their interactions, by providing very well-defined data. AmyloGraph, an online database presenting information on amyloid-amyloid interactions, is available at (). Its functionalities are also accessible as the R package (). AmyloGraph is the only publicly available repository for experimentally determined amyloid-amyloid interactions

Building Babies - Chapter 16

In contrast to birds, male mammals rarely help to raise the offspring. Of all mammals, only among rodents, carnivores, and primates, males are sometimes intensively engaged in providing infant care (Kleiman and Malcolm 1981). Male caretaking of infants has long been recognized in nonhuman primates (Itani 1959). Given that infant care behavior can have a positive effect on the infant’s development, growth, well-being, or survival, why are male mammals not more frequently involved in “building babies”? We begin the chapter defining a few relevant terms and introducing the theory and hypotheses that have historically addressed the evolution of paternal care. We then review empirical findings on male care among primate taxa, before focusing, in the final section, on our own work on paternal care in South American owl monkeys (Aotus spp.). We conclude the chapter with some suggestions for future studies.Deutsche Forschungsgemeinschaft (HU 1746/2-1) Wenner-Gren Foundation, the L.S.B. Leakey Foundation, the National Geographic Society, the National Science Foundation (BCS-0621020), the University of Pennsylvania Research Foundation, the Zoological Society of San Dieg

It takes two: Evidence for reduced sexual conflict over parental care in a biparental canid

In biparental systems, sexual conflict over parental investment predicts that the parent providing care experiences greater reproductive costs. This inequality in parental contribution is reduced when offspring survival is dependent on biparental care. However, this idea has received little empirical attention. Here, we determined whether mothers and fathers differed in their contribution to care in a captive population of coyotes (Canis latrans). We performed parental care assays on 8 (n = 8 males, 8 females) mated pairs repeatedly over a 10-week period (i.e., 5–15 weeks of litter age) when pairs were first-time breeders (2011), and again as experienced breeders (2013). We quantified consistent individual variation (i.e., repeatability) in 8 care behaviors and examined within- and among-individual correlations to determine if behavioral plasticity within or parental personality across seasons varied by sex. Finally, we extracted hormone metabolites (i.e., cortisol and testosterone) from fecal samples collected during gestation to describe potential links between hormonal mechanisms and individual consistency in parental behaviors. Parents differed in which behaviors were repeatable: mothers demonstrated consistency in provisioning and pup-directed aggression, whereas fathers were consistent in pup checks. However, positive within-individual correlations for identical behaviors (e.g., maternal versus paternal play) suggested that the rate of change in all behaviors except provisioning was highly correlated between the sexes. Moreover, positive among-individual correlations among 50% of identical behaviors suggested that personality differences across parents were highly correlated. Lastly, negative among-individual correlations among pup-directed aggression, provisioning, and gestational testosterone in both sexes demonstrated potential links between preparental hormones and labile parental traits. We provide novel evidence that paternal contribution in a biparental species reaches near equivalent rates of their partners

The procedure for electing the pope as the supreme authority of the Catholic Church

Celem pracy magisterskiej była analiza procedury wyboru papieża w Kościele Katolickim. Praca opiera się na konstytucji Universi Dominici Gregis jako głównym źródle prawnym charakteryzującym procedurę głosowania. Ponad to w pracy znajduje się historia papiestwa od początków pojawienia się tej instytucji do czasów obecnych. Przytoczona jest również historia konklawe i charakterystyka tej instytucji na przestrzeni wieków. Praca magisterska skupia się również na powstałych problemach współczesnego świata w kontekście papiestwa i konstytucji. Porusza problem abdykacji papieża analizując rezygnację Benedykta XVI.The aim of the master's thesis was to analyze the procedure of electing the pope in the Catholic Church. This is based on the constitution of Universi Dominici Gregis as the main legal source characterizing the voting procedure. In addition, the work includes the history of the papacy from the beginning of this institution to the present day. The history of the conclave and the characteristics of this institution over the centuries are also quoted. The master's thesis also focuses on the emerging problems of the modern world in the context of the papacy and the constitution. It raises the problem of the Pope's abdication by analyzing the resignations of Benedict XVI

Assessing the Differential Effects of Pre-existing Verbal Relations, Pay for Performance, and Rules on Cooperative Responding

Prior research on cooperation in a business environment has primarily relied upon financial consequences to increase or decrease cooperative responding. When results indicate otherwise, a post-hoc attribution to social or verbal contingencies is usually made. The purpose of this study was to assess the participatory effect of pre-existing verbal relations and rules on cooperative behavior under different pay for performance conditions. The Implicit Relational Assessment Procedure (IRAP) and Mixed-Trial IRAP (MT-IRAP) were utilized to account for the existing derived relations among verbal stimuli (D. Barnes-Holmes et al., 2006; Levin, 2010). More specifically, Experiment 1 utilized the MT-IRAP to select potential motivational stimuli for Experiment 2. In the second experiment, the IRAP was utilized to assess participants' pre-existing social biases. One week following the IRAP, the same participants were exposed to rule statements under either piece rate or profit-share conditions in a reversal design. Results indicated minimal impact of pre-existing social biases on cooperative behavior, however the rule statements had a significant effect on responding, particularly under financially neutral conditions (profit share). The potential role of rules as verbal establishing stimuli (i.e., motivative augmentals) and their application in organizations are discussed

Patient’s electronic record – geriatrics clinic’

Tematem niniejszej pracy jest „Elektroniczny rekord pacjenta – klinika geriatrii”, na który składa się system zbudowany z interfejsów webowych oraz aplikacji mobilnej działającej na tablecie i tekstowy opis dzieła.Do napisania systemu wykorzystano język C# i środowisko programistyczne Visual Studio 2017. Projekty zrealizowano w oparciu o technologie firmy Microsoft. Implementacje aplikacji mobilnej pracującej na systemie Android wykonano przy pomocy technologii Xamarin. Projekt został zbudowany z trzech modułów, z których dwa odpowiadają za komunikacje z serwerem i wymianę danych, a trzeci za działanie aplikacji. W części mobilnej, zastosowano wzorzec programistyczny Model-View-Presenter (MVP). Realizacja projektu interfejsów webowych wykonana została w technologii ASP.NET WebAPI. Projekt rozdzielono na sześć modułów, z których każdy odpowiada za poszczególną funkcjonalność systemu od obsługi bazy danych po udostępnienie interfejsów WebAPI umożliwiających wymianę danych z klientem. W tym przypadku zostały wykorzystane różne biblioteki umożliwiające np. wstrzykiwanie zależności, mapowanie danych, narzędzia ORM i inne. Komunikacja między klientem a serwerem jest możliwa dzięki zastosowaniu architektury REST w aplikacji działającej na serwerze. Wymiana danych odbywa się w formacie JSON.Tekstowy opis pracy w pierwszym rozdziale szczegółowo opisuje cele pracy, które zostały postawione przed jej wykonaniem. Drugi rozdział, objaśnia technologie i narzędzia wykorzystane w pracy, z kolei trzeci opisuje implementację zrealizowanych aplikacji. Ostatni rozdział zawiera wnioski końcowe, powstałe po zrealizowaniu tematu pracy.The topic of this graduate thesis is ‘Patient’s electronic record – Geriatrics Clinic’. Project consist of WebAPI interfaces, mobile application operated by tablet and textual part.The system has been written using C# language and programming environment Visual Studio 2017. The projects have been realized applying Microsoft technologies. Implementations of mobile application, which is working on Android System, are based on Xamarin technology. Project is divided into three modules. Two of them are connected with communication and data exchange with server. Third one answers for application functioning. In a mobile part has been used programming pattern Model-View-Presenter. WebAPI interfaces employ ASP.NET WebAPI technology. This project constists of six modules, each of them handle a task relevant to system functionality – from database service to sharing WebAPI interfaces enabled exchanging data with client. In that instance have been used various frameworks, what permit a lot of options, for example, dependency injection, data mapping, ORM tools and so forth. Communication between client and server is possible due to REST architecture, which is used in project functioning on server. Data swapping based on JSON format.The textual part consists of four sections. First of them is detailed depiction of aims of this study. Next section explicate process and tools which have been used. Third section describe implementation of realized applications. The last section allude to final conclusions, which developed after completion of the thesis subject